Transposable elements (TEs) play a crucial role in genomic regulation by affecting gene functions, particularly in alternative splicing (AS). Among these, intronic TEs are notably abundant in the human genome, numbering over a million instances. Current research has predominantly fixated on individual TEs near splicing sites, neglecting the vast majority of deep intronic TEs. This oversight hampers our understanding of their collective impact on AS and their relevance to developmental and disease phenotypes. To address this gap, we first start with examining the interaction of TEs within the TBXT gene. TBXT is vital in embryonic development and implicated in tail loss in hominoids and chordoma, a bone cancer where TBXT is aberrantly activated. Exploring these interactions will deepen our knowledge of AS regulation and provide insights into personalized cancer treatment by identifying new genetic markers and therapeutic targets. This research seeks to provide a novel framework to study how the interaction between TEs can affect gene function by modulating pre-mRNA splicing. By uncovering the intricacies of TE-induced AS, we seek to unearth new genetic markers and therapeutic targets, offering novel avenues in disease treatment and prevention.